Currently, the only input objects supported are image objects. However, the
current framework allows for warping of other objects such as meshes and point
sets.

-r, --reference-image imageFileName

For warping input images, the reference image defines the spacing, origin, size,
and direction of the output warped image.

-o, --output warpedOutputFileName

[warpedOutputFileName or compositeDisplacementField,<printOutCompositeWarpFile=0>]

Linear[genericAffineTransformFile,<calculateInverse=0>]

One can either output the warped image or, if the boolean is set, one can print
out the displacement field based on the composite transform and the reference
image. A third option is to compose all affine transforms and (if boolean is
set) calculate its inverse which is then written to an ITK file

Several interpolation options are available in ITK. These have all been made
available.

-t, --transform transformFileName

[transformFileName,useInverse]

Several transform options are supported including all those defined in the ITK
library in addition to a deformation field transform. The ordering of the
transformations follows the ordering specified on the command line. An identity
transform is pushed onto the transformation stack. Each new transform
encountered on the command line is also pushed onto the transformation stack.
Then, to warp the input object, each point comprising the input object is warped
first according to the last transform pushed onto the stack followed by the
second to last transform, etc. until the last transform encountered which is the
identity transform. Also, it should be noted that the inverse transform can be
accommodated with the usual caveat that such an inverse must be defined by the
specified transform class

-f, --default-value value

Default voxel value to be used with input images only. Specifies the voxel value
when the input point maps outside the output domain